Hi all,
I am trying to run the BaseRecalibrator in GATK but got an error message of:
MESSAGE: SAM/BAM file SAMFileReader{test.sorted.bam} is malformed: The input .bam file contains reads with no platform information. First observed at read with name = 552_2035_733_F
I am assuming that this is telling me that I need the platform information to be contained in the read group (SOLiD sequencing in this case). I was under the impression that it is not necessary to have this information in the file, or am I mistaken by this? Should having this information really matter? Or am I missing some flag that should be added that will skip this.
Thanks
I am trying to run the BaseRecalibrator in GATK but got an error message of:
MESSAGE: SAM/BAM file SAMFileReader{test.sorted.bam} is malformed: The input .bam file contains reads with no platform information. First observed at read with name = 552_2035_733_F
I am assuming that this is telling me that I need the platform information to be contained in the read group (SOLiD sequencing in this case). I was under the impression that it is not necessary to have this information in the file, or am I mistaken by this? Should having this information really matter? Or am I missing some flag that should be added that will skip this.
Thanks
Comment